3vn5: Difference between revisions
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==Crystal structure of Aquifex aeolicus RNase H3== | ==Crystal structure of Aquifex aeolicus RNase H3== | ||
<StructureSection load='3vn5' size='340' side='right' caption='[[3vn5]], [[Resolution|resolution]] 1.98Å' scene=''> | <StructureSection load='3vn5' size='340' side='right'caption='[[3vn5]], [[Resolution|resolution]] 1.98Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vn5]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3vn5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VN5 FirstGlance]. <br> | ||
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1768, rnhC ([ | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1768, rnhC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn5 OCA], [https://pdbe.org/3vn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vn5 RCSB], [https://www.ebi.ac.uk/pdbsum/3vn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vn5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/RNH3_AQUAE RNH3_AQUAE]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[ | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Aquae]] | [[Category: Aquae]] | ||
[[Category: Large Structures]] | |||
[[Category: Ribonuclease H]] | [[Category: Ribonuclease H]] | ||
[[Category: Angkawidjaja, C]] | [[Category: Angkawidjaja, C]] | ||
Revision as of 21:53, 27 July 2022
Crystal structure of Aquifex aeolicus RNase H3Crystal structure of Aquifex aeolicus RNase H3
Structural highlights
Function[RNH3_AQUAE] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Publication Abstract from PubMedThe crystal structure of ribonuclease H3 from Aquifex aeolicus (Aae-RNase H3) was determined at 2.0 A resolution. Aae-RNase H3 consists of an N-terminal TATA box-binding protein (TBP)-like domain (N-domain) and a C-terminal RNase H domain (C-domain). The structure of the C-domain highly resembles that of Bacillus stearothermophilus RNase H3 (Bst-RNase H3), except that it contains three disulfide bonds, and the fourth conserved glutamate residue of the Asp-Glu-Asp-Glu active site motif (Glu198) is located far from the active site. These disulfide bonds were shown to contribute to hyper-stabilization of the protein. Non-conserved Glu194 was identified as the fourth active site residue. The structure of the N-domain without the C-domain also highly resembles that of Bst-RNase H3. However, the arrangement of the N-domain relative to the C-domain greatly varies for these proteins because of the difference in the linker size between the domains. The linker of Bst-RNase H3 is relatively long and flexible, while that of Aae-RNase H3 is short and assumes a helix formation. Biochemical characterizations of Aae-RNase H3 and its derivatives without the N- or C-domain or with a mutation in the N-domain indicate that the N-domain of Aae-RNase H3 is important for substrate binding, and uses the flat surface of the beta-sheet for substrate binding. However, this surface is located far from the active site and on the opposite side to the active site. We propose that the N-domain of Aae-RNase H3 is required for initial contact with the substrate. The resulting complex may be rearranged such that only the C-domain forms a complex with the substrate. Structure and characterization of RNase H3 from Aquifex aeolicus.,Jongruja N, You DJ, Angkawidjaja C, Kanaya E, Koga Y, Kanaya S FEBS J. 2012 Aug;279(15):2737-53. doi: 10.1111/j.1742-4658.2012.08657.x. Epub, 2012 Jul 3. PMID:22686566[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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